Multiscale molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer

The topology (gro) and trajectory (xtc) files for multiscale - coarse-grained (CG) and atomistic (AT) molecular dynamics simulations of human P-glycoprotein in complex lipid bilayer. The coarse grained simulations are 10 microseconds long and the trajectories have 1 frame saved at every 10 ns, while the atomistic simulations are 100 ns long and have 2 frames saved at every nanosecond

Fractional interaction matrix of the outer and inner leaflet of the plasma membrane.

<p>The matrix shows the fractional interaction as the relative number of contacts between lipids compared to all other contacts. If a lipid has more than one contact with another lipid this interaction is only counted once. Two lipids are defined as being in contact if the distance between the glycerol ester moiety and amino alcohols is less than 11 Å. Since cholesterol flip-flops between the leaflets during simulations it is not possible to assign these to specific leaflets and has therefore been omitted from this analysis. A fully random distribution of between four lipid types would result in a fraction of 0.25. (A) Fractional interaction of the lipids within the outer leaflet. (B) Fractional interaction of inner leaflet lipids.</p

Ligand Binding in the Extracellular Vestibule of the Neurotransmitter Transporter Homologue LeuT

The human monoamine transporters (MATs) facilitate the reuptake of monoamine neurotransmitters from the synaptic cleft. MATs are linked to a number of neurological diseases and are the targets of both therapeutic and illicit drugs. Until recently, no high-resolution structures of the human MATs existed, and therefore, studies of this transporter family have relied on investigations of the homologues bacterial transporters such as the leucine transporter LeuT, which has been crystallized in several conformational states. A two-substrate transport mechanism has been suggested for this transporter family, which entails that high-affinity binding of a second substrate in an extracellular site is necessary for the substrate in the central binding site to be transported. Compelling evidence for this mechanism has been presented, however, a number of equally compelling accounts suggest that the transporters function through a mechanism involving only a single substrate and a single high-affinity site. To shed light on this apparent contradiction, we have performed extensive molecular dynamics simulations of LeuT in the outward-occluded conformation with either one or two substrates bound to the transporter. We have also calculated the substrate binding affinity in each of the two proposed binding sites through rigorous free energy simulations. Results show that substrate binding is unstable in the extracellular vestibule and the substrate binding affinity within the suggested extracellular site is very low (0.2 and 3.3 M for the two dominant binding modes) compared to the central substrate binding site (14 nM). This suggests that for LeuT in the outward-occluded conformation only a single high-affinity substrate binding site exists

Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

<div><p>The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from <i>Aquifex Aoelicus</i>. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design.</p></div

Binding of serotonin to the extracellular binding pocket of hSERT.

<p>A representative pose of serotonin binding in the extracellular binding site as obtained from induced fit docking. Serotonin is shown in purple spheres, and noribogaine (in the central binding pocket) is shown in orange spheres. TM1 (red), TM3 (blue), TM6 (green) and TM8 (yellow) are shown in cartoon. The amino acid residues in the extracellular gate are shown in orange sticks. TM2, TM4, TM5, TM7 and TM9 are shown as beige cylinders.</p